Overlapping surfaces problem
You probably need to delete the faces and reconstruct that part of the model from scratch, try selecting the overlapping faces, press X and select "Only Faces", this way it deletes only the faces, leaving the edges and the vertices, then you can repair the model by recreating the faces, selecting the vertices you want and pressing F. Keep in mind that you probably need to delete some of the edges too, because it's likely that some of them are intersecting each other as well; in that case after you press X select "Only Edges &amp; Faces" so that it only deletes the edge, leaving the vertices intact.